Sourdough Bacteria: The Complete Guide to What Lives in Your Starter

Every mature sourdough starter is a tiny ecosystem — a living community of bacteria and wild yeasts working together to leaven bread and develop flavour. Here is what actually lives in a starter, and what each organism contributes to your loaf.

The two families that matter

A sourdough starter is not a single organism. It is a symbiotic community, and two families dominate: lactic acid bacteria (LAB) and wild yeasts. Every starter has a slightly different composition depending on the flour, the water, the temperature of your kitchen and how you feed it — but the fundamentals are the same everywhere in the world.

The bacteria: Lactobacillus & Fructilactobacillus

The bacterial workhorses of a mature sourdough starter come from a group historically called Lactobacillus. In 2020, an international taxonomy review split the old Lactobacillus genus into 25 new genera. As part of that split, the species most famous for sourdough was renamed:

• Old name: Lactobacillus sanfranciscensis
• New name: Fructilactobacillus sanfranciscensis

It is exactly the same organism — the reclassification simply reflects newer DNA-based taxonomy. Most bakers and older recipes still use the historical name; scientific papers from 2020 onwards use the new one. Both refer to the bacterium first isolated from San Francisco sourdough in 1971.

What Lactobacillus sanfranciscensis does

This is the bacterium behind the signature San Francisco tang. Two key features make it special:

1. It ferments maltose specifically. Most bacteria prefer glucose, but flour releases maltose when its enzymes break down starch. L. sanfranciscensis is one of the few LAB species that can consume maltose efficiently, which gives it a huge competitive advantage in a starter environment.
2. It produces both lactic and acetic acid. Lactic acid gives sourdough its milky, yoghurt-like tang. Acetic acid gives it a sharper, vinegar-like note. The ratio depends on hydration, temperature and feeding schedule — cooler and stiffer starters lean towards acetic; warmer and wetter ones favour lactic.

Other bacteria commonly found in sourdough

• Levilactobacillus brevis (formerly Lactobacillus brevis) — very common in European sourdough starters. Also heterofermentative (produces lactic + acetic acid + CO2).
• Limosilactobacillus fermentum — a heat-tolerant species often found in warmer starters.
• Fructilactobacillus sanfranciscensis — the San Francisco strain we described above.
• Companilactobacillus paralimentarius — occasionally isolated from long-lived European starters.

The yeasts: wild Saccharomyces

Wild yeasts do the leavening. They are not the same as the commercial dried yeast (Saccharomyces cerevisiae baker's strain) you might buy in a sachet — although some starters do contain that species. Common sourdough yeasts include:

• Kazachstania humilis — one of the most frequently identified yeasts in sourdough starters worldwide. Grows well alongside L. sanfranciscensis.
• Saccharomyces cerevisiae — same species as commercial yeast but as a wild strain, adapted to your kitchen.
• Torulaspora delbrueckii — occasionally dominant in slower, colder-fermented starters.

The yeasts consume glucose released by the bacteria's activity and produce CO2 gas — that is what makes the loaf rise. They also produce trace ethanol and small amounts of aromatic compounds that contribute to sourdough's complex flavour.

Why symbiosis matters

The bacteria and yeasts in a starter are not just cohabiting — they actively help each other. The bacteria produce acids that lower the pH to around 3.8. That acidity keeps mould and unwanted bacteria out of the culture, while the wild yeasts happily tolerate it. In return, the yeasts break down some sugars the bacteria cannot easily access on their own. The balance is remarkable, and the community can persist for decades or even centuries with regular feeding.

How to encourage the right community

• Feed with a mix of white and wholegrain flour. Wholegrain flour has more of the enzymes that release maltose, which favours L. sanfranciscensis.
• Keep the starter at room temperature (20-25°C) during active use. This is the temperature range where the sourdough microbial community is most competitive against unwanted organisms.
• Feed on a consistent schedule. Regular feeding gives the beneficial community time to establish and maintain its edge over transient microorganisms.
• Do not skip feeds for weeks at a time at room temperature. The starter will still be alive, but the balance of species can shift. Refrigerate if you need a break.

How can you tell what is in your starter?

You cannot tell by taste or smell alone. The only reliable method is laboratory analysis — typically 16S rRNA sequencing for the bacteria and ITS sequencing for the yeasts. Commercial suppliers that market lab-verified starters should be able to show you the sequencing report.

Our own Dough Dough Fast Start Sourdough Starter has been independently tested at a UK laboratory and confirmed to contain Fructilactobacillus sanfranciscensis. That means the same bacterium behind classical San Francisco sourdough is producing the tang in your loaves.

References

1. Kline, L. & Sugihara, T. F. (1971). Microorganisms of the San Francisco sour dough bread process. II. Applied Microbiology, 21(3), 459-465.
2. Zheng, J. et al. (2020). A taxonomic note on the genus Lactobacillus: Description of 23 novel genera. International Journal of Systematic and Evolutionary Microbiology, 70(4), 2782-2858.
3. Gänzle, M. G. (2014). Enzymatic and bacterial conversions during sourdough fermentation. Food Microbiology, 37, 2-10.